0.1% of a house's value seems like a fair amount of money. I doubt it would seem strange to put a lot of effort into getting that much money, if it was framed differently.
Admittedly, not spending 2-3 months to work out another deal is worth quite a lot of money as well. But this behaviour doesn't seem obviously irrational.
0.1% of a house's value is almost certainly not an appreciable amount of money. It's so low that, if the parties could not find a way to come to terms over it, the agents may swallow it themselves just to get the deal done.
For a half-million dollar home, which would be a relatively nice house for most of the country, you're talking about $500. For any party on that transaction (buyer, seller or their respective agents who each stand to make $15k on a normal 3% commission), that's not a lot of money and is almost certainly not worth arguing over if you're in all but the earliest stages of negotiation.
Admittedly, not spending 2-3 months to work out another deal is worth quite a lot of money as well. But this behaviour doesn't seem obviously irrational.